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INTERACTS_PiP

Last Updated

Current

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node_web_buttons_proteindomain copy 2.png

Description

An interaction between two proteins.

Properties

  • methods - IntAct method(s) for determining interaction with ID and name (ex ["MI:0007"(anti tag coimmunoprecipitation),..]). VirHost method(s) with name (ex [(two hybrid),...]).

  • typesIntAct interaction type(s) with ID and name (ex ["MI:0915"(physical association),..]). VirHost interaction type(s) with name (ex [(physical association),...]).

  • miscores - The MIscore normalized score calculates a composite score for an interaction based on the number of publications reporting the interaction, the reported interaction detection methods and interaction types. (IntAct and/or VirHost depending on sources)

  • is_directedIntAct edges can be directed

  • pubmedIDspubmed ID(s) (IntAct)

  • roleA - Role of start protein (ex [enzyme]) (IntAct)

  • roleB - Role of end protein (ex [enzyme target]) (IntAct)

  • confidence - Maximum miscore (IntAct) or score (STRING)

  • domainInteraction - True if domain interaction (ProtCID)

  • experiments_score - All interaction records from the IMEx databases (plus BioGRID), are re-mapped and re-processed: first, duplicate records and datasets are removed, and then entire groups of records are benchmarked against KEGG and scored accordingly. (1; STRING)

  • textmining_score - Statistical co-citation analysis across a large number of scientific texts, including all PubMed abstracts as well as OMIM (1; STRING)

  • databases_score - Manually curated interaction records assembled by expert curators, at KEGG, Reactome, BioCyc and Gene Ontology, as well as legacy datasets from PID and BioCarta. (1; STRING

  • score - Total score using all STRING scores

  • neighborhood_score - Gene neighborhood based interaction prediction (1, 2; STRING)

  • coexpression_score - Generated from gene-by-gene correlation tests across a large number of gene expression datasets (using both transcriptome measurements as well as proteome measurements). (1; STRING)

  • cooccurrence_score - Co-occurrence of pairs of genes across multiple genomes used for interaction prediction (1, 2; STRING)

  • exp_score -  Combined known interactions score using database and experimental STRING scores 

  • fusion_score - Fusion events used for interaction prediction (1, 2; STRING)

  • MISCORE - To be deleted using miscores

  • Interaction_Type - To be deleted using types

  • Interaction_Detection_Method - To be deleted using methods

  • source - To be deleted using sources

  • sourcesIntAct, ProtCID, STRING, and VirHost

  1. Szklarczyk, Damian, et al. "STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets." Nucleic acids research 47.D1 (2019): D607-D613.

  2. Snel, Berend, et al. "STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene." Nucleic acids research 28.18 (2000): 3442-3444.


Updates

V5        2,195,834 edges

V4        1,018,665 edges

V3        1,017,557 edges

V2        1,017,557 edges

V1        1,048,666 edges

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